Without actually knowing what Ferguson said, which you haven't quoted but I assume will, there's no way to relate the two incidents. Mancini's remark was more a joke, from what I read, and would be unlikely to be taken as an insult. If Ferguson said something more serious then perhaps it niggled the guy. Was it the ref himself who brought the complaint, or the FA? Or the Refs Union?
Many managers make comments about refs, although they are being more careful these days, I'm thinking Mick McCarthy when he was in charge of Wolves here. But most can make a comment and not get into trouble over it, so whatever SIr Alex said must have been pretty tough for the ref to take offence, or whoever did.
As I said, I haven't got the facts and don't really have the time to go researching, but I have seen that when United win the game in, say, the 96th or 97th minute, Fergie has no problem with extra added time --- even though it's often hard to justify where so much has come from --- but if it happens and goes against him he's asking where did all that extra time come from? It's swings and roundabouts, and evens itself out over the course of a season, more or less. To quote yourself, he can't have it both ways. Extra time happens, and if it doesn't benefit Man U then that's just tough. I do wonder though how many last-minute/second winning goals Man U have scored over the last few seasons? And could that extra time be accounted for? What is the rule: a minute for each substitution and then whatever for injuries leading to delays? Never quite sure of that.
Anyway, I'm just bitter cos I support a **** side who are heading towards the 11:50 slot on BBC next season!
And I'm old and crotchety...